Fossils are a window into the past. They force us to confront questions about the world as it was thousands, or even millions, of years ago. Fossils reveal that what we see around us today is but a tiny sample of the abundant diversity of organisms that God has created. That diversity includes entire ecosystems of plants and animals that passed from this world long before humans could lay eyes on them. Fossils are the traces of God’s past activity, preserved to reveal his glory and to humble us in our exploration of creation.
The Genome: A book that records God’s acts of creation
For hundreds of years, fossils in the form of altered remains of bones, shells, and teeth, along with impressions of footprints and leaf surfaces, were all that we had that could speak to us of God’s creativity with living things over time. Over the past 20 years, we have developed new tools to look into the past. These tools include our ability to obtain the genetic code of organisms. By prying open the genome, we aren’t just looking at ourselves in the here and now, but we are also opening a new history book–one that records God’s creative acts throughout the long ages of Earth’s history.
Our genomes, and those of all other organisms, contain records of historic encounters with viruses, bacteria, and even inter-relations with other species. We can now search the genome for preserved relics of the past, much as we search the rocks for evidence of past life. We call the artifacts that are found in the former searches genomic or molecular fossils.
What are molecular fossils and what can we learn from them?
Molecular fossils are portions of a genome that are remnants of dead genes or other genetic elements inserted into a genome from a foreign source. The former originated by the loss of function, which can be thought of as the “death” of a gene. But loss of function isn’t usually followed by an immediate loss from the genome, and therefore, these genomic elements have been passed on, from parent to offspring, to the present day. During those countless transmissions, these pieces of the genome accumulate errors through mutation, making it harder and harder to recognize their ancestors. In this way, they are like fossils extracted from the ground in that they can start out as very clear impressions of something or contain much of the original materials, but over time they are compressed, eroded, or chemically altered—which makes them more difficult to identify.
Molecular fossils are like little time capsules inside the genomes of all organisms. They tell us a story of an organism’s past, just like a fossil in a rock can tell us a story such as the evolutionary history of a lineage that shares fossils (see Dennis Venema’s Evolution Basicsseries for example).
Because of astounding technological advances in sequencing DNA, it is possible to analyze the entire genome of hundreds of organisms. As a result, we can search through the hundreds of billions of pieces of the genomes of thousands of organisms to find pieces of a DNA sequence that represent remnants of a “fossilized” coding sequence These genetic sequences might have been useful in the past but are no longer needed by the organism. Every animal, plant, and human contains many of these discarded pieces, like old memories left to gradually fade away. While most memories fade over time, many still exist, and we can still go back and dig up those memories to reconstruct past events. That is just what paleogenomics attempts to do: dig through our genetic memories to learn about past events that shaped us.
Molecular fossils are found in all genomes
We now recognize that genomes of all organisms contain pieces of old discarded genes and remains of viral infections. As an example of the former, remains of the sweet taste gene are found in vampire bats even though they do not taste sugar. This fossil gene attests to a time in the past when the gene was functional—like a time before those bats had taken up, i.e. evolved, their blood drinking habits.
These nonfunctional fossil genes, often referred to as pseudogenes, that I have described above are extremely common. And so, in a way, they are a bit boring—like abundant fossils shells found in marine rocks. These molecular fossils can be easily found and identified by students learning molecular techniques for the first time.
Even more provocatively, we can even look at footprints of long past interactions of our genomes with viruses. These molecular fossil hunters called paleovirologists search for more exotic molecular fossils. For example, paleoviriologists have dug through the genomes of animals to find past encounters with the Ebola virus. They have discovered degraded fragments of the Ebola virus in bats and a number of rodents. By looking at how degraded those fragments are and where they have been inserted into the host genomes, they have determined that the Ebola virus active today has been around for at least 16 million years. These studies have helped us to learn how the Ebola virus has evolved, which in turn is teaching us how to produce better defenses against it.
Another example of paleovirology comes from the hunt for a molecular fossil of the Herpes virus in the genome of several primates. The discovery of a dead Herpes virus embedded in the genome of some primates shows us that viruses we think of as simply parasites on individual cells may become invasive in the genomes of their hosts. By inserting themselves into the genome they become part of that genome’s history.
Today, we are learning that all organisms carry some record of relics of successful viral insertions into their genome.
Paleovirologists have plenty of material to work with. Each of us carries with us hundreds of thousands of pieces of viral genomes, which exist as fossilized viral relics of past infections of our ancestors. Once inserted into an ancestor those viral genomes have been passed down to all of us today. Each time we pass these viruses to our children, though, we are apt to make mistakes in the copying process, causing it to be more and more difficult to recognize these molecular fossils over time. Despite this loss of genetic memory, about 8% of each of our genomes has been identified as pieces of ancient viral infections. With a genome of about three billion nucleotides (ATCGs) this means that all of us are carrying around at least 240 million nucleotides in our genome that are not really “human.” Don’t worry, the vast majority of this DNA is no longer functional and isn’t likely to have any effect on us.
This is a companion discussion topic for the original entry at https://biologos.org/blog/paleogenomics-a-new-generation-of-fossil-hunters-dig-up-gods-story-of-creat